The Whitewater Mennonite Church was organized on 18 April 1927 by Mennonite families from the Soviet Union who settled in that community in 1924. The first elder was Franz F. Enns of Lena, Manitoba, who had been elder of the Terek Mennonite Church. On 16 June 1938 G. G. Neufeld succeeded him.

In 1931 the church had six congregations led by Elder Franz F. Enns and assisted by 14 ministers. The church had 452 congregational members, a total of 964 members and adherents, and 187 families.

In 1958 the congregation had 565 members and a total population of 1,209 persons in 257 families. It had six congregations at that time: Whitewater (162 members), Rivers (96 members), Ninga (63 members), Lena (80 members), Crystal City (135 members), Manitou (29 members). Five of these groups had their own meetinghouses. In 1958 all worship was in German.

The Elder performed all baptisms and observed the Lord's Supper four times annually with all congregations. Footwashing was practiced at one time, but was dropped.